LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -39.712312 0.0000000) to (10.808322 39.712312 7.0757080) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6321382 4.4124792 4.7171386 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -39.712312 0.0000000) to (10.808322 39.712312 7.0757080) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6321382 4.4124792 4.7171386 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.712312 0.0000000) to (10.808322 39.712312 7.0757080) create_atoms CPU = 0.000 seconds 254 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 506 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_608695023236_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.822 | 4.822 | 4.822 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1980.3499 0 -1980.3499 65073.514 57 0 -2100.5968 0 -2100.5968 12193.766 Loop time of 4.10792 on 1 procs for 57 steps with 506 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1980.34993998037 -2100.59470893242 -2100.59677233436 Force two-norm initial, final = 211.93681 0.18377973 Force max component initial, final = 59.223142 0.028534874 Final line search alpha, max atom move = 1.0000000 0.028534874 Iterations, force evaluations = 57 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1012 | 4.1012 | 4.1012 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030057 | 0.0030057 | 0.0030057 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003762 | | | 0.09 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29296.0 ave 29296 max 29296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29296 Ave neighs/atom = 57.897233 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.822 | 4.822 | 4.822 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -2100.5968 0 -2100.5968 12193.766 6074.12 68 0 -2101.08 0 -2101.08 -389.59827 6116.1257 Loop time of 0.507383 on 1 procs for 11 steps with 506 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2100.59677233436 -2101.07977466833 -2101.08004456949 Force two-norm initial, final = 106.44467 2.8886905 Force max component initial, final = 103.37626 2.2350807 Final line search alpha, max atom move = 0.0054623473 0.012208787 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50546 | 0.50546 | 0.50546 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000291 | 0.000291 | 0.000291 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001635 | | | 0.32 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29104.0 ave 29104 max 29104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29104 Ave neighs/atom = 57.517787 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2101.08 0 -2101.08 -389.59827 Loop time of 2.03e-06 on 1 procs for 0 steps with 506 atoms 147.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.03e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29076.0 ave 29076 max 29076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29076 Ave neighs/atom = 57.462451 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2101.08 -2101.08 10.794674 80.224784 7.0624973 -389.59827 -389.59827 -177.63888 -406.74874 -584.4072 2.2686572 402.47703 Loop time of 2.106e-06 on 1 procs for 0 steps with 506 atoms 142.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.106e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2339.00 ave 2339 max 2339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14538.0 ave 14538 max 14538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29076.0 ave 29076 max 29076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29076 Ave neighs/atom = 57.462451 Neighbor list builds = 0 Dangerous builds = 0 506 -2101.08004456949 eV 2.26865717781843 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04